Recently, cholinium cation amino acid anion ILs, a new type of bio-ILs, have been reported to pretreat biomass with great efficiency at temperatures lower than 100 oC. In order to understand the mechanism and the role of cations and anions on biomass pretreatment efficiency, we selected four ILs with different combinations of cations: 1-ethyl-3-methylimidazolium ([C2mim]) vs. cholinium ([Ch]) and anions: acetate ([OAc]) vs. lysinate ([Lys]). The results indicate that ILs with [Lys] anion perform better than [OAc] anion in terms of delignification and sugar production at pretreatment temperatures lower than 100 oC. The Kamlet-Tamft parameters indicate that both [C2mim][Lys] and [Ch][Lys] have much higher hydrogen bonding basicity (β value) than the ILs with [OAc] a characteristic we hypothesize is directly related to sugar yield.